{"id":29414947,"url":"https://github.com/arnikz/piqmie","last_synced_at":"2026-02-03T22:35:17.009Z","repository":{"id":55152542,"uuid":"42406525","full_name":"arnikz/PIQMIe","owner":"arnikz","description":"Proteomics Identifications \u0026 Quantitations Data Management \u0026 Integration Service","archived":false,"fork":false,"pushed_at":"2025-01-31T15:52:25.000Z","size":98382,"stargazers_count":1,"open_issues_count":2,"forks_count":0,"subscribers_count":1,"default_branch":"master","last_synced_at":"2025-09-04T22:44:24.653Z","etag":null,"topics":["data-analysis","data-management","data-visualisation","mass-spectrometry","peptide-identification","protein-inference","protein-quantification","proteomics","silac","web-application"],"latest_commit_sha":null,"homepage":"https://www.research-software.nl/software/piqmie","language":"HTML","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"apache-2.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/arnikz.png","metadata":{"files":{"readme":"README.md","changelog":"CHANGELOG.md","contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":"CITATION.cff","codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":".zenodo.json"}},"created_at":"2015-09-13T17:57:03.000Z","updated_at":"2025-01-28T10:27:33.000Z","dependencies_parsed_at":"2025-04-12T04:29:34.550Z","dependency_job_id":null,"html_url":"https://github.com/arnikz/PIQMIe","commit_stats":null,"previous_names":[],"tags_count":2,"template":false,"template_full_name":null,"purl":"pkg:github/arnikz/PIQMIe","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/arnikz%2FPIQMIe","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/arnikz%2FPIQMIe/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/arnikz%2FPIQMIe/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/arnikz%2FPIQMIe/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/arnikz","download_url":"https://codeload.github.com/arnikz/PIQMIe/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/arnikz%2FPIQMIe/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":29060578,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-02-03T22:28:58.191Z","status":"ssl_error","status_checked_at":"2026-02-03T22:28:56.515Z","response_time":96,"last_error":"SSL_connect returned=1 errno=0 peeraddr=140.82.121.5:443 state=error: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["data-analysis","data-management","data-visualisation","mass-spectrometry","peptide-identification","protein-inference","protein-quantification","proteomics","silac","web-application"],"created_at":"2025-07-11T15:18:12.658Z","updated_at":"2026-02-03T22:35:16.995Z","avatar_url":"https://github.com/arnikz.png","language":"HTML","funding_links":[],"categories":[],"sub_categories":[],"readme":"# PIQMIe\n\n[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.594144.svg)](https://doi.org/10.5281/zenodo.594144)\n[![Published in NAR](https://img.shields.io/badge/published%20in-NAR-blue.svg)](https://doi.org/10.1093/nar/gku478)\n[![CI](https://github.com/arnikz/PIQMIe/actions/workflows/ci.yaml/badge.svg?branch=dev)](https://github.com/arnikz/PIQMIe/actions/workflows/ci.yaml)\n\n## Description\n\n_PIQMIe_ is a web-based tool for reliable analysis and visualization of semi-quantitative mass spectrometry (MS)-based proteomics data. _PIQMIe_ readily integrates peptide and (non-redundant) protein identifications and quantitations, as obtained by the [MaxQuant/Andromeda](http://maxquant.org/) software ([Cox _et al._, 2008](https://doi.org/10.1038/nbt.1511), [2011](https://doi.org/10.1021/pr101065j)), with additional biological information from the [UniProtKB](http://www.uniprot.org/) database, and makes the linked data available in the form of a light-weight relational database ([SQLite](http://sqlite.org/)). Using the web interface, users are presented with a concise summary of their proteomics experiments in numerical and graphical forms, as well as with a searchable protein grid and interactive visualization tools to aid in the rapid assessment of the experiments and in the identification of proteins of interest. _PIQMIe_ provides data access via a web interface and programmatic RESTful API.\n\n## Prerequisites\n- [Docker CE](https://docs.docker.com/install/)\n\n## Software stack\n- perl\n- python\n  - cherrypy\n  - genshi\n  - cairo\n- sqlite\n- javascript/css\n  - jquery\n  - d3.js\n  - bootstrap\n\n## Install\n\n**1. Clone this repository.**\n\n```bash\ngit clone https://github.com/arnikz/PIQMIe.git\n```\n\n**2. Build and deploy web app.**\n\n```bash\ncd PIQMIe\ndocker build -t piqmie .\ndocker run -d -p 8080:8080 piqmie\n```\n\n## Usage\n\nTo view the [sample data](/data) on your local PIQMIe instance, follow _Sample Data_ tab and click on [results](http://localhost:8080/results/a000000000000000000000000000000000000001).\n\nAlternatively, upload your own data files, i.e., MaxQuant peptide (`evidence.txt`) and protein (`proteinGroups.txt`) lists including the sequence library in FASTA (`.fa|fasta`), to the web server and click on the _Submit_ button to process the input files. After processing, click on the generated link to view the results. Note: For each session, a new (sub)directory `\u003cDATA_DIR\u003e/\u003cjobID\u003e` including I/O files will be created.\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Farnikz%2Fpiqmie","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Farnikz%2Fpiqmie","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Farnikz%2Fpiqmie/lists"}